#!/usr/bin/env Rscript

suppressPackageStartupMessages(library("optparse"))
suppressPackageStartupMessages(library("phyloseq"))

option_list <- list(
    make_option(c("--input"), action = "store", dest = "input", help = "Input RDS file containing a phyloseq object"),
    make_option(c("--output"), action = "store", dest = "output", help = "Output PDF")
)

parser <- OptionParser(usage = "%prog [options] file", option_list = option_list);
args <- parse_args(parser, positional_arguments = TRUE);
opt <- args$options;

phyloseq_obj <- readRDS(opt$input);

# Start PDF device driver and generate the plot.
dev.new();
pdf(file = opt$output);
plot_richness(phyloseq_obj, x = "samples", color = "samples");
dev.off()